The objective of this project was to determine the major features of mammalian mitochondrial DNA sequence variation and eveolution as it reflects on the underlying mechanisms of mutation. Human mitochondrial DNA sequence comparisons were made, resulting in the detection of high frequencies of multiple (repeated) nucleotide substitutions and insertions/deletions. Two substitution biases were apparent, one favoring transitions by a factor of 32:1 over transversions and the other favoring a high rate of turnover of purines relative to pyrimidines on the heavy strand of mtDNA. Their occurrence in coding and noncoding regions as well as ribosomal RNA and transfer RNA genes suggests that these phenomena may result from biases in the mutational pathways since it is unlikely that similar selective constraints would exist in these functionally very different regions. We have also modeled the dynamics of the substitution process in mammalian mtDNA. We have studied the temporal behavior of several quantities and compared the model's predictions with estimates obtained from recent mtDNA sequence data for an increasingly divergent series of primates, the mouse and the cow. Our results are consistent with the hypothesis that the decrease in the proportion of transitions observed as divergence increases is a consequence of the highly biased substitution process. In addition, our results support the hypothesis that while a portion of the mtDNA molecule evolves at an extremely rapid rate, a significant portion of the molecule is under strong selective constraints related to conservation of protein sequence and transfer RNA secondary structure.